Hello Yikan-- > > I have predicted a model of an RNA which is made up with two > independent domains. I want to generated a conformational pool by > Xplor-NIH, then I can pick out the representative ensemble by the > EOM. This conformational sampling process may related bigger > molecular translation and rotation which can make sure to sample all > the possible solution conformations of the RNA; I do not know how to > set the simulation parameters. Do someone have tried to do that? >
I have not done exactly this, but I can probably help. I assume you want to model the domains as rigid bodies and allow only linker motion. Two possibilities might be a) perform torsion-angle MD with large timesteps, or b) use some sort of sampling technique to randomly set torsion angles (and possibly exclude conformations containing clashes). What you choose may depend on the length of the linker. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
